@@ -7,3 +7,4 @@ appveyor.yml

 docs

 mkdocs

 .gitmodules

+.github

@@ -1,7 +1,7 @@

 Package: ggtree

 Type: Package

 Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

-Version: 1.7.8

+Version: 1.7.9

 Authors@R: c(

 	   person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph")),

 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = c("aut", "ths")),

@@ -1,5 +1,12 @@

+CHANGES IN VERSION 1.7.9

+------------------------

+ o fixed geom_tiplab(geom='label') <2017-03-02, Thu>

+   + https://github.com/GuangchuangYu/ggtree/issues/115

+

 CHANGES IN VERSION 1.7.8

 ------------------------

+ o get_taxa_name now sorted by taxa position and also support whole tree <2017-03-01, Wed>

+ o unrooted layout support branch.length="none", fixed #114 <2017-03-01, Wed>

  o remove apeBootstrap and raxml object support as they were removed from treeio <2017-02-28, Tue>

 CHANGES IN VERSION 1.7.7

@@ -1,4 +1,4 @@

-##' get taxa name of a selected node

+##' get taxa name of a selected node (or tree if node=NULL) sorted by their position in plotting

 ##'

 ##'

 ##' @title get_taxa_name

@@ -7,16 +7,20 @@

 ##' @return taxa name vector

 ##' @export

 ##' @author Guangchuang Yu

-get_taxa_name <- function(tree_view=NULL, node) {

+get_taxa_name <- function(tree_view=NULL, node=NULL) {

     tree_view %<>% get_tree_view

     df <- tree_view$data

-    sp <- get.offspring.df(df, node)

-    res <- df[sp, "label"]

-    return(res[df[sp, "isTip"]])

-}

-

+    if (!is.null(node)) {

+        sp <- get.offspring.df(df, node)

+        df <- df[sp, ]

+    }

+    with(df, {

+        i = order(y, decreasing=T)

+        label[i][isTip[i]]

+    })

+}

 ##' view a clade of tree

@@ -6,6 +6,7 @@

 ##' @param data A layer specific dataset -

 ##'             only needed if you want to override he plot defaults.

 ##' @param ... other arguments passed on to 'layer'

+##' @param position The position adjustment to use for overlapping points on this layer

 ##' @param family sans by default, can be any supported font

 ##' @param parse if TRUE, the labels will be passd into expressions

 ##' @param nudge_x horizontal adjustment

@@ -25,6 +26,7 @@

 ##' @author Guangchuang Yu

 geom_label2 <- function(mapping = NULL, data = NULL,

                         ...,

+                        position = "identity",

                         family = "sans",

                         parse = FALSE,

                         nudge_x = 0,

@@ -36,8 +38,6 @@ geom_label2 <- function(mapping = NULL, data = NULL,

                         show.legend = NA,

                         inherit.aes = TRUE) {

-    position = "identity"

-

     if (!missing(nudge_x) || !missing(nudge_y)) {

         if (!missing(position)) {

             stop("Specify either `position` or `nudge_x`/`nudge_y`", call. = FALSE)

@@ -5,13 +5,13 @@

 ##' @param mapping the aesthetic mapping

 ##' @param data A layer specific dataset -

 ##'             only needed if you want to override he plot defaults.

+##' @param ... other arguments passed on to 'layer'

 ##' @param position The position adjustment to use for overlapping points on this layer

 ##' @param family sans by default, can be any supported font

 ##' @param parse if TRUE, the labels will be passd into expressions

 ##' @param na.rm logical

 ##' @param show.legend logical

 ##' @param inherit.aes logical

-##' @param ... other arguments passed on to 'layer'

 ##' @param nudge_x horizontal adjustment

 ##' @param nudge_y vertical adjustment

 ##' @param check_overlap if TRUE, text that overlaps previous text in the same layer will not be plotted

@@ -24,9 +24,16 @@

 ##' \link[ggplot2]{geom_text}

 ##' @author Guangchuang Yu

 geom_text2 <- function(mapping = NULL, data = NULL,

-                       position = "identity", family="sans", parse = FALSE,

-                       na.rm=TRUE, show.legend = NA, inherit.aes = TRUE,

-                       ..., nudge_x = 0, nudge_y = 0, check_overlap = FALSE) {

+                       ...,

+                       position = "identity",

+                       family="sans",

+                       parse = FALSE,

+                       na.rm=TRUE,

+                       show.legend = NA,

+                       inherit.aes = TRUE,

+                       nudge_x = 0,

+                       nudge_y = 0,

+                       check_overlap = FALSE) {

     if (!missing(nudge_x) || !missing(nudge_y)) {

         if (!missing(position)) {

@@ -494,7 +494,7 @@ fortify.phylo <- function(model, data, layout="rectangular",

 as.data.frame.phylo <- function(x, row.names, optional,

                                 layout="rectangular", ...) {

     if (layout == "unrooted") {

-        return(layout.unrooted(x))

+        return(layout.unrooted(x, ...))

     }

     as.data.frame.phylo_(x, layout, ...)

 }

@@ -159,7 +159,7 @@ reroot_node_mapping <- function(tree, tree2) {

 ##' @importFrom ape reorder.phylo

-layout.unrooted <- function(tree) {

+layout.unrooted <- function(tree, branch.length="branch.length", ...) {

     N <- getNodeNum(tree)

     root <- getRoot(tree)

@@ -198,7 +198,12 @@ layout.unrooted <- function(tree) {

             alpha <- (end - start) * ntip.child/curNtip

             beta <- start + alpha / 2

-            length.child <- df[child, "length"]

+            if (branch.length == "none") {

+                length.child <- 1

+            } else {

+                length.child <- df[child, "length"]

+            }

+

             df[child, "x"] <- df[curNode, "x"] + cospi(beta) * length.child

             df[child, "y"] <- df[curNode, "y"] + sinpi(beta) * length.child

             df[child, "angle"] <- -90 -180 * beta * sign(beta - 1)

@@ -1,8 +1,6 @@

-

-

 ##' @importFrom ggplot2 last_plot

 get_tree_view <- function(tree_view) {

     if (is.null(tree_view))

@@ -2,9 +2,9 @@

 ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

 ===========================================================================================================================

-[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.9-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.8-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-22537/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1894/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />

+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.9-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.9-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-22704/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1894/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />

-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--02--28-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--03--02-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)

@@ -51,7 +51,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/

 ### Download stats

-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-22537/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1894/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-22704/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1894/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

          ++--------------------+--------------------+--------------------+--------------------+--------+

          |                                                                                        *    |

@@ -4,10 +4,10 @@

 \alias{geom_label2}

 \title{geom_label2}

 \usage{

-geom_label2(mapping = NULL, data = NULL, ..., family = "sans",

-  parse = FALSE, nudge_x = 0, nudge_y = 0, label.padding = unit(0.25,

-  "lines"), label.r = unit(0.15, "lines"), label.size = 0.25,

-  na.rm = TRUE, show.legend = NA, inherit.aes = TRUE)

+geom_label2(mapping = NULL, data = NULL, ..., position = "identity",

+  family = "sans", parse = FALSE, nudge_x = 0, nudge_y = 0,

+  label.padding = unit(0.25, "lines"), label.r = unit(0.15, "lines"),

+  label.size = 0.25, na.rm = TRUE, show.legend = NA, inherit.aes = TRUE)

 }

 \arguments{

 \item{mapping}{the aesthetic mapping}

@@ -17,6 +17,8 @@ only needed if you want to override he plot defaults.}

 \item{...}{other arguments passed on to 'layer'}

+\item{position}{The position adjustment to use for overlapping points on this layer}

+

 \item{family}{sans by default, can be any supported font}

 \item{parse}{if TRUE, the labels will be passd into expressions}

@@ -4,10 +4,9 @@

 \alias{geom_text2}

 \title{geom_text2}

 \usage{

-geom_text2(mapping = NULL, data = NULL, position = "identity",

+geom_text2(mapping = NULL, data = NULL, ..., position = "identity",

   family = "sans", parse = FALSE, na.rm = TRUE, show.legend = NA,

-  inherit.aes = TRUE, ..., nudge_x = 0, nudge_y = 0,

-  check_overlap = FALSE)

+  inherit.aes = TRUE, nudge_x = 0, nudge_y = 0, check_overlap = FALSE)

 }

 \arguments{

 \item{mapping}{the aesthetic mapping}

@@ -15,6 +14,8 @@ geom_text2(mapping = NULL, data = NULL, position = "identity",

 \item{data}{A layer specific dataset -

 only needed if you want to override he plot defaults.}

+\item{...}{other arguments passed on to 'layer'}

+

 \item{position}{The position adjustment to use for overlapping points on this layer}

 \item{family}{sans by default, can be any supported font}

@@ -27,8 +28,6 @@ only needed if you want to override he plot defaults.}

 \item{inherit.aes}{logical}

-\item{...}{other arguments passed on to 'layer'}

-

 \item{nudge_x}{horizontal adjustment}

 \item{nudge_y}{vertical adjustment}

@@ -4,7 +4,7 @@

 \alias{get_taxa_name}

 \title{get_taxa_name}

 \usage{

-get_taxa_name(tree_view = NULL, node)

+get_taxa_name(tree_view = NULL, node = NULL)

 }

 \arguments{

 \item{tree_view}{tree view}

@@ -15,7 +15,7 @@ get_taxa_name(tree_view = NULL, node)

 taxa name vector

 }

 \description{

-get taxa name of a selected node

+get taxa name of a selected node (or tree if node=NULL) sorted by their position in plotting

 }

 \author{

 Guangchuang Yu